TABLE 1.

Proteins identified by MS/MS after depolymerization of purified sheaths with DTT and formic acid

A sample lacking the formic acid treatment was included to distinguish the amyloid proteins from contaminants. The latter are equally abundant in treated and untreated samples. The major sheath protein (MspA) is highlighted in bold type and is identified by its increased abundance in the formic acid-treated sample as evident from the emPAI score. The major contaminating proteins are gas vesicle proteins, which are known to form amyloid-like structures on the surface of gas vesicles (42). An abundant S layer-related protein, which shows similar abundance in the formic acid treated and untreated samples, is furthermore observed. FA, formic acid.

RefSeq accession nb	Protein description	Molecular massa	Mascot score		Protein sequence coverage		Spectral MS/MS counts (Mascot)		emPAI (Mascot)b
			0% FA	100% FA	0% FA	100% FA	0% FA	100% FA	0% FA	100% FA
		kDa			%
YP_843493	Putative uncharacterized protein	61.1	164	2534	18	77	17	158	0.11	7.51
YP_842502	Gas vesicle structural protein	8	0	496	0	98	0	20	0	11.75
YP_842503	Gas vesicle structural protein	7.8	0	498	0	98	0	23	0	12.16
YP_843107	S layer-related duplication domain	79.8	1031	1441	24	24	125	139	1.72	5.58
YP_842724	Acetyl-CoA decarbonylase/synthase gamma subunit	53.3	86	43	39	46	12	14	0.05	0.06
YP_842729	Acetyl-CoA decarbonylase/synthase complex subunit α	91.1	323	431	28	39	80	109	0.47	0.88
YP_843615	Acetyl-coenzyme A synthetase	74.5	405	560	29	37	59	87	0.67	1.26
YP_843000	Methyl-coenzyme M reductase, α subunit	61.8	127	180	47	54	26	23	0.36	0.76
YP_843003	Methyl-coenzyme M reductase, β subunit	46	167	204	36	54	35	34	0.41	0.41

^a The gel migration generally correlated well with the molecular weights of the identified proteins.

^b The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantitation of the proteins in a mixture based on protein coverage by the peptide matches in a database search result (73).